Analysis of the algorithm: From kernels to prioritized genes.

Kernelization section

The algorithm transformed the semantic similarity matrix to make it compatible with a kernel. Once this was done for each network and kernel type, it was integrated by kernel type. Below there is a general analysis of the properties of each matrix in the different phases of the process.

Annotations properties

Table 1. Annotation files descriptors

Net Min Max Average Standard_Deviation
DepMap_effect 972 17354 2043.6562906724512 3829.1218209282715
biological_process 1 1053 8.255678448065316 20.730757162592834
cellular_component 1 5172 7.219656420451649 82.56741928666138
disease 1 81 1.7829472267615112 2.3512948371338793
gene_PS 1 108 2.1519058295964126 5.045578888786698
gene_TF 1 5778 3.0320060963993143 74.46796191948712
gene_hgncGroup 1 2294 2.261042369703787 23.27548667222241
hippie_ppi 1 2985 84.68724915097252 150.1286010250888
molecular_function 1 6791 4.87167748867193 54.08093332133869
pathway 1 479 6.75436035343834 16.179001796162975
phenotype 1 1307 23.941396322320227 48.71098651648341
string_ppi 1 7338 610.0699285559645 500.6662722348227

Matrix properties

Table 2. Similarity matrixes

Net Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
DepMap_effect_bicor_sim 17354x17354 301161316 106761316 0.35449876968926514
DepMap_effect_pearson_sim 17354x17354 301161316 84855920 0.2817623495841013
DepMap_effect_spearman_sim 17354x17354 301161316 194719108 0.6465608219084817
biological_process_sim 16979x16979 288286441 256362631 0.8892635744877089
cellular_component_sim 17963x17963 322669369 320867108 0.9944145271502359
disease_sim 4162x4162 17322244 17228280 0.9945755295907389
gene_PS_sim 362x362 131044 1666 0.012713287140197186
gene_TF_sim 1044x1044 1089936 172858 0.15859463307937346
gene_hgncGroup_sim 25136x25136 631818496 14457654 0.022882606462980154
hippie_ppi_sim 19434x19434 377680356 1630698 0.0043176669744507444
molecular_function_sim 17333x17333 300432889 296572456 0.9871504314562578
pathway_sim 3429x3429 11758041 159182 0.013538139559132342
phenotype_sim 5077x5077 25775929 25699341 0.9970287006920294
string_ppi_sim 18476x18476 341362576 11271627 0.03301951588272523

Table 3. Filtered similarity matrixes

Net Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
biological_process_sim 12099x12099 146385801 120006262 0.8197944143503372
cellular_component_sim 89x89 7921 6388 0.806463830324454
hippie_ppi_sim 15763x15763 248472169 408340 0.0016434033704595704
molecular_function_sim 1656x1656 2742336 2732263 0.9963268541856286
phenotype_sim 2187x2187 4782969 4717473 0.9863064134431981
string_ppi_sim 16111x16111 259564321 480917 0.001852785460448549

Table 4. Uncombined kernel matrixes

Net Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
DepMap_effect_bicor ct 17354x17354 301161316 301161316 1.0
DepMap_effect_bicor el 17354x17354 301161316 301161316 1.0
DepMap_effect_bicor ka 17354x17354 301161316 106778670 0.35455639329189276
DepMap_effect_bicor rf 17354x17354 301161316 301161316 1.0
DepMap_effect_pearson ct 17354x17354 301161316 301161316 1.0
DepMap_effect_pearson el 17354x17354 301161316 301161316 1.0
DepMap_effect_pearson ka 17354x17354 301161316 84855920 0.2817623495841013
DepMap_effect_pearson rf 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman ct 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman el 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman ka 17354x17354 301161316 194719108 0.6465608219084817
DepMap_effect_spearman rf 17354x17354 301161316 301161316 1.0
biological_process ct 12099x12099 146385801 146385801 1.0
biological_process el 12099x12099 146385801 146385801 1.0
biological_process ka 12099x12099 146385801 120010285 0.8198218965239669
biological_process rf 12099x12099 146385801 146385801 1.0
cellular_component ct 89x89 7921 7921 1.0
cellular_component el 89x89 7921 7921 1.0
cellular_component ka 89x89 7921 6473 0.8171947986365358
cellular_component node2vec 89x89 7921 7921 1.0
cellular_component rf 89x89 7921 7921 1.0
disease ct 4162x4162 17322244 17322244 1.0
disease el 4162x4162 17322244 17322244 1.0
disease ka 4162x4162 17322244 17230892 0.9947263183684516
disease rf 4162x4162 17322244 17322244 1.0
gene_PS ct 362x362 131044 111955 0.8543313696163121
gene_PS el 362x362 131044 7680 0.05860626964988859
gene_PS ka 362x362 131044 2028 0.015475718079423705
gene_PS node2vec 362x362 131044 131044 1.0
gene_PS rf 362x362 131044 7680 0.05860626964988859
gene_TF ct 1044x1044 1089936 1089918 0.9999834852688598
gene_TF el 1044x1044 1089936 1062998 0.9752847873636618
gene_TF ka 1044x1044 1089936 173902 0.15955248748550374
gene_TF node2vec 1044x1044 1089936 1089936 1.0
gene_TF rf 1044x1044 1089936 1062998 0.9752847873636618
gene_hgncGroup ct 25136x25136 631818496 631304330 0.9991862124909999
gene_hgncGroup el 25136x25136 631818496 326932198 0.5174463870079549
gene_hgncGroup ka 25136x25136 631818496 14482790 0.022922390040319426
gene_hgncGroup rf 25136x25136 631818496 326932198 0.5174463870079549
hippie_ppi ct 15763x15763 248472169 248472161 0.9999999678032352
hippie_ppi el 15763x15763 248472169 245768483 0.9891187571997249
hippie_ppi ka 15763x15763 248472169 421467 0.0016962342370022132
hippie_ppi node2vec 15763x15763 248472169 248472169 1.0
hippie_ppi rf 15763x15763 248472169 245768483 0.9891187571997249
molecular_function ct 1656x1656 2742336 2742336 1.0
molecular_function el 1656x1656 2742336 2742336 1.0
molecular_function ka 1656x1656 2742336 2733178 0.9966605113304862
molecular_function rf 1656x1656 2742336 2742336 1.0
pathway ct 3429x3429 11758041 11744213 0.9988239537521599
pathway el 3429x3429 11758041 8641125 0.7349119636510878
pathway ka 3429x3429 11758041 162611 0.013829769772022398
pathway node2vec 3429x3429 11758041 11758041 1.0
pathway rf 3429x3429 11758041 8641125 0.7349119636510878
phenotype ct 2187x2187 4782969 4782969 1.0
phenotype el 2187x2187 4782969 4782969 1.0
phenotype ka 2187x2187 4782969 4718455 0.9865117252484806
phenotype rf 2187x2187 4782969 4782969 1.0
string_ppi ct 16111x16111 259564321 259564321 1.0
string_ppi el 16111x16111 259564321 252333871 0.9721438987756719
string_ppi ka 16111x16111 259564321 497009 0.0019147816544478006
string_ppi node2vec 16111x16111 259564321 259564321 1.0
string_ppi rf 16111x16111 259564321 252333871 0.9721438987756719

Table 5. Integrated kernel matrixes

Integration Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
integration_mean_by_presence ct 29867x29867 892037689 779232361 0.8735419709379566
integration_mean_by_presence el 29867x29867 892037689 544165899 0.6100256813252203
integration_mean_by_presence ka 29867x29867 892037689 149003403 0.16703711607413932
integration_mean_by_presence node2vec 18083x18083 326994889 315076927 0.9635530633630179
integration_mean_by_presence rf 29867x29867 892037689 544165899 0.6100256813252203
mean ct 29867x29867 892037689 779232361 0.8735419709379566
mean el 29867x29867 892037689 544165899 0.6100256813252203
mean ka 29867x29867 892037689 149003403 0.16703711607413932
mean node2vec 18083x18083 326994889 315076927 0.9635530633630179
mean rf 29867x29867 892037689 544165899 0.6100256813252203

Weight values